Loading report..

Highlight Samples

Regex mode off

    Rename Samples

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      Regex mode off

        Explain with AI

        Configure AI settings to get explanations of plots and data in this report.

        Keys entered here will be stored in your browser's local storage. See the docs.

        Anonymize samples off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
        Settings are automatically saved. You can also save named configurations below.

        Save Settings

        You can save the toolbox settings for this report to the browser or as a file.

        Load Settings

        Choose a saved report profile from the browser or load from a file:

          Load from File

        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.29

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/diseasemodulediscovery analysis pipeline. For information about how to interpret these results, please see the documentation.
        Report generated on 2025-08-19, 14:59 UTC based on data in: /home/johannes/workspace/network_medicine_drug_repurposing_tutorial/nextflow_pipeline/work/51/e7fabed3b5dcd31e2f36d85ba16c20

        General Statistics

        Showing 7/7 rows and 11/11 columns.
        Sample NameNodesEdgesSeedsDiameterComponentsLargest componentMax distance to seedIsolated nodesRobustness (seeds permutation)Seed rediscoverySeed rediscovery (normalized)
        seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.diamond
        215
        1321
        15
        5
        11
        204
        3
        8
        0.86
        0.00
        0.0000
        seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.domino
        13
        12
        5
        2
        3
        8
        1
        0
        0.89
        0.07
        0.0074
        seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.firstneighbor
        1004
        4218
        15
        7
        2
        1002
        1
        0
        0.94
        0.13
        0.0001
        seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.no_tool
        15
        5
        15
        0
        14
        2
        0
        9
        seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.robust
        70
        97
        15
        8
        3
        64
        2
        0
        0.89
        0.07
        0.0012
        seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.robust_bias_aware
        74
        97
        15
        11
        1
        74
        3
        0
        0.89
        0.07
        0.0012
        seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.rwr
        104
        236
        15
        9
        1
        104
        2
        0
        0.91
        0.13
        0.0015

        WARNING: Modules not visualized

        List of modules with too many nodes for visualization. The maximum number of nodes can be adjusted with the '--visualization_max_nodes' parameter.

        Showing 1/1 rows.
        ModuleNodes
        seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.firstneighbor
        1004

        WARNING: Modules too large for Drugst.One

        List of modules with too many nodes for Drugst.One export and drug prioritization. The maximum number of nodes can be adjusted with the '--drugstone_max_nodes' parameter.

        Showing 1/1 rows.
        ModuleNodes
        seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.firstneighbor
        1004

        Input

        Shows the number of seeds retained from the input files and the number of seeds removed (not in network)..

        Network

        Showing 1/1 rows and 7/7 columns.
        NetworkNodesEdgesDiameterComponentsLargest componentSelf loopsDuplicate edges
        filtered_ppi_only_reviewed_proteins_solution
        12797
        95916
        10
        101
        12651
        1175
        0

        Seeds

        Created with MultiQC

        Overlap

        Jaccard similarity between the gene sets of the modules, excluding the seeds.

        Jaccard similarity

        Created with MultiQC

        Jaccard similarity (without seeds)

        Created with MultiQC

        Shared nodes

        Created with MultiQC

        Shared nodes (without seeds)

        Created with MultiQC

        Robustness (seeds permutation)

        Jaccard index distributions between the original and permuted modules.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        BIOPAX_PARSERgraph-tool2.77 (commit 4ad25c62, )
        nedrex0.1.4
        pybiopax0.1.4
        python3.12.7
        BIOPAX_VALIDATORbiopax-validator/biopax-validator/lib/biopax-validator-6.0.0-SNAPSHOT.jar
        javaopenjdk version "20.0.2.1" 2023-08-22
        DIAMONDpython3.8.5
        DOMINO_DOMINOpython3.6.15
        DOMINO_SLICERpython3.6.15
        DRUGPREDICTIONSdrugstone0.4.5
        pandas2.2.3
        python3.12.7
        DRUGSTONEEXPORTgraph-tool2.77 (commit 4ad25c62, )
        python3.12.7
        FIRSTNEIGHBORgraph-tool2.77 (commit 4ad25c62, )
        python3.12.7
        GPROFILER2_GOSTr-ggplot23.4.3
        r-gprofiler20.2.2
        GRAPHTOOLPARSERgraph-tool2.77 (commit 4ad25c62, )
        python3.12.7
        MODULEPARSERgraph-tool2.77 (commit 4ad25c62, )
        python3.12.7
        NETWORKANNOTATIONgraph-tool2.77 (commit 4ad25c62, )
        python3.12.7
        ROBUSTpython3.10.4
        ROBUSTBIASAWAREpython3.10.14
        robust-bias-aware0.0.1
        RWRpython3.12.7
        SAVEMODULESgraph-tool2.77 (commit 4ad25c62, )
        pandas2.2.3
        python3.12.7
        SEEDPERMUTATIONpython3.12.7
        SEEDPERMUTATIONEVALUATIONpython3.12.7
        TOPOLOGYgraph-tool2.77 (commit 4ad25c62, )
        python3.12.7
        VISUALIZEMODULESgraph-tool2.77 (commit 4ad25c62, )
        networkx3.3
        pyintergraph1.3.3
        python3.12.7
        pyvis0.3.1
        VISUALIZEMODULESDRUGSgraph-tool2.77 (commit 4ad25c62, )
        networkx3.3
        pyintergraph1.3.3
        python3.12.7
        pyvis0.3.1
        WorkflowNextflow24.10.5
        nf-core/diseasemodulediscoveryv1.0dev-g8cec67b

        nf-core/diseasemodulediscovery Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/diseasemodulediscovery

        Methods

        Data was processed using nf-core/diseasemodulediscovery v1.0dev of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v24.10.5 (Di Tommaso et al., 2017) with the following command:

        nextflow run nf-core/diseasemodulediscovery -r dev -profile docker --seeds ../data/NeDRex_api/seed_genes_huntingtons_disease.csv --network ../data/NeDRex_api/filtered_ppi_only_reviewed_proteins_solution.csv --id_space uniprot --skip_digest --outdir results --run_seed_permutation -resume

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        nf-core/diseasemodulediscovery Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/diseasemodulediscovery

        Input/output options

        id_space
        uniprot
        network
        ../data/NeDRex_api/filtered_ppi_only_reviewed_proteins_solution.csv
        outdir
        results
        seeds
        ../data/NeDRex_api/seed_genes_huntingtons_disease.csv

        Module evaluation

        run_seed_permutation
        true
        skip_digest
        true

        Generic options

        trace_report_suffix
        2025-08-19_16-54-30

        Core Nextflow options

        configFiles
        /home/johannes/.nextflow/assets/nf-core/diseasemodulediscovery/nextflow.config, /home/johannes/workspace/network_medicine_drug_repurposing_tutorial/nextflow_pipeline/nextflow.config
        container
        ghcr.io/repo4eu/modulediscovery_python_dependencies:v0.1.0
        containerEngine
        docker
        launchDir
        /home/johannes/workspace/network_medicine_drug_repurposing_tutorial/nextflow_pipeline
        profile
        docker
        projectDir
        /home/johannes/.nextflow/assets/nf-core/diseasemodulediscovery
        revision
        dev
        runName
        shrivelled_lagrange
        userName
        johannes
        workDir
        /home/johannes/workspace/network_medicine_drug_repurposing_tutorial/nextflow_pipeline/work

        MultiQC v1.29 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.